title: The Caenorhabditis elegans intermediate-size transcriptome shows high degree of stage-specific expression.
abstract: Earlier studies have revealed a substantial amount of transcriptional activity occurring outside annotated protein-coding genes of the Caenorhabditis elegans genome. One important fraction of this transcriptional activity relates to intermediate-size (70-500 nt) transcripts (is-ncRNAs) of mostly unknown function. Profiling the expression of this segment of the transcriptome on a tiling array through the C. elegans life cycle identified 5866 hitherto unannotated transcripts. The novel loci were distributed across intronic and intergenic space, with some enrichment toward protein-coding gene termini. The majority of the putative is-ncRNAs showed either stage-specific expression, or distinct developmental variation in their expression levels. More than 200 loci showed male-specific expression, and conserved loci were significantly enriched on the X chromosome, both observations strongly suggesting involvement of is-ncRNAs in sex-specific functions. Half of the novel loci were conserved in other nematodes, and numerous loci showed significant conservational correlations to nearby coding genes. Assuming functional roles for most of the novel loci, the data imply a nematode is-ncRNA tool kit of considerable size and variety.
authors.affiliation: Bioinformatics Laboratory and National Laboratory of Biomacromolecules, Institute of Biophysics, Chinese Academy of Sciences, Beijing 100101, China.
authors.forename: Yunfei
authors.initials: Y
authors.lastname: Wang
authors.forename: Jingjing
authors.initials: J
authors.lastname: Chen
authors.forename: Guifeng
authors.initials: G
authors.lastname: Wei
authors.forename: Housheng
authors.initials: H
authors.lastname: He
authors.forename: Xiaopeng
authors.initials: X
authors.lastname: Zhu
authors.forename: Tengfei
authors.initials: T
authors.lastname: Xiao
authors.forename: Jiao
authors.initials: J
authors.lastname: Yuan
authors.forename: Bo
authors.initials: B
authors.lastname: Dong
authors.forename: Shunmin
authors.initials: S
authors.lastname: He
authors.forename: Geir
authors.initials: G
authors.lastname: Skogerbø
authors.forename: Runsheng
authors.initials: R
authors.lastname: Chen
mesh_terms: D000818:Animals; D001483:Base Sequence; D017173:Caenorhabditis elegans / Q000235:genetics* / Q000254:growth & development / Q000378:metabolism; D020869:Gene Expression Profiling; D056426:Genetic Loci; D049751:Genome, Helminth; D008297:Male; D008969:Molecular Sequence Data; D018510:RNA, Helminth / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D022661:RNA, Untranslated / Q000737:chemistry / Q000235:genetics / Q000378:metabolism*; D012091:Repetitive Sequences, Nucleic Acid
chemical_list: D018510:RNA, Helminth; D022661:RNA, Untranslated